GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08235 in Herbaspirillum seropedicae SmR1

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate HSERO_RS08275 HSERO_RS08275 branched-chain amino acid transporter permease subunit LivH

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS08275 HSERO_RS08275
           branched-chain amino acid transporter permease subunit
           LivH
          Length = 308

 Score =  360 bits (923), Expect = e-104
 Identities = 183/299 (61%), Positives = 230/299 (76%), Gaps = 3/299 (1%)

Query: 6   QQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWV 65
           QQL+NGLSLGAIY LIAIGYTMVYGIIGMINFAHGEIYMI ++V L+T  AIG      +
Sbjct: 10  QQLVNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIASYVGLVTLTAIGVQSGYPL 69

Query: 66  PLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGAR 125
           PL L   L+ S+L T +YGWTVER+AYRPLR  PRL PLISAIGMSIFLQNYVQI QGAR
Sbjct: 70  PLLLGGALIVSVLVTGLYGWTVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQIGQGAR 129

Query: 126 SKPLQPILPGNLTLMDGA---VSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQ 182
              +  ++ G L    G+   V++ Y R+  + +T+ LM   T  I R+ +GRA RAC +
Sbjct: 130 DMSVPVLISGALEFQMGSDFTVTIPYSRMVIVGVTLVLMVALTLFIARSRMGRACRACAE 189

Query: 183 DKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLG 242
           D  MA LLG++ ++VIS TFV+GA LAAV G+++ L  G ++ YIGF+AG+KAFTAAVLG
Sbjct: 190 DMGMANLLGIDTNKVISFTFVLGAMLAAVGGVLIALTIGKLNPYIGFIAGIKAFTAAVLG 249

Query: 243 GIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIEKV 301
           GIGS+PGAMLGGV++GL E F +GY+ SE+KDV +F +LVL+L+FRPTGLLG+P++EKV
Sbjct: 250 GIGSIPGAMLGGVLLGLAETFAAGYLPSEYKDVVSFGLLVLILLFRPTGLLGKPDVEKV 308


Lambda     K      H
   0.329    0.144    0.425 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 425
Number of extensions: 22
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 301
Length of database: 308
Length adjustment: 27
Effective length of query: 274
Effective length of database: 281
Effective search space:    76994
Effective search space used:    76994
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory